KRAS Mutation Subtypes and Their Association with Other Driver Mutations in Oncogenic Pathways.

The KRAS mutation stands out as one of the most influential oncogenic mutations, which directly regulates the hallmark features of cancer and interacts with other cancer-causing driver mutations. However, there remains a lack of precise information on their cooccurrence with mutated variants of KRAS and any correlations between KRAS and other driver mutations. To enquire about this issue, we delved into cBioPortal, TCGA, UALCAN, and Uniport studies. We aimed to unravel the complexity of KRAS and its relationships with other driver mutations. We noticed that G12D and G12V are the prevalent mutated variants of KRAS and coexist with the TP53 mutation in PAAD and CRAD, while G12C and G12V coexist with LUAD. We also noticed similar observations in the case of PIK3CA and APC mutations in CRAD. At the transcript level, a positive correlation exists between KRAS and PIK3CA and between APC and KRAS in CRAD. The existence of the co-mutation of KRAS and other driver mutations could influence the signaling pathway in the neoplastic transformation. Moreover, it has immense prognostic and predictive implications, which could help in better therapeutic management to treat cancer.

Experimental and Theoretical Investigation of Reactions of Formyl (HCO) Radicals in the Gas Phase: (I) Kinetics of HCO Radicals with Ethyl Formate and Ethyl Acetate in Tropospherically Relevant Conditions.

Formyl (HCO) radicals were generated in situ in the gas phase via the photolysis of glyoxal in N2 at 248 nm using the pulsed laser photolysis-cavity ring-down spectrometry technique, and the absorption cross-section of the radical was measured to be σHCO = (5.3 ± 0.9) × 10-19 cm2 molecule-1 at 298 K and 615.75 nm, which was the probing wavelength. The kinetics of the reactions of HCO radicals with ethyl formate (EF) and ethyl acetate (EA) were investigated experimentally in the temperature range of 260-360 (±2) K at a pressure of 60 Torr/N2. The absolute rate coefficient for the reaction between HCO and EF was measured to be kHCO+EFExpt(298 K) = (1.39 ± 0.30) × 10-14 cm3 molecule-1 s-1 at ambient temperature, whereas that for the reaction of HCO with EA was measured tobe kHCO+EATheory(298 K) = (2.05 ± 0.43) × 10-14 cm3 molecule-1 s-1. The reaction of HCO with EA was faster than that with EF, which might be due to the greater stability of the formed radical intermediate due to hyperconjugative and inductive effects. The dependency of the measured kinetics on experimental pressures and laser fluences was examined within a certain range. To complement the experiments, kinetics of the title reactions in the temperature range of 200-400 K were deciphered theoretically via the canonical variational transition-state theory with small-curvature tunneling and interpolated single-point energy (CVT/SCT/ISPE) method using a dual-level approach at the CCSD(T)/cc-pVTZ//MP2/6-311++G(d,p) level of theory/basis set. A good degree of agreement was detected between the rate coefficients measured experimentally and those calculated theoretically both at room temperature and throughout the range of temperatures studied. The kinetic branching ratios and thermochemistry of the reactions were investigated to understand the thermodynamic feasibility and kinetic lability of each pathway throughout the studied temperatures. Atmospheric implications of these reactions of HCO radicals are also discussed.

A Combined Experimental and Theoretical Study to Determine the Kinetics of 2-Ethoxy Ethanol with OH Radical in the Gas Phase.

The reactivity of 2-ethoxy ethanol with OH radicals was experimentally measured in the temperature range of 278-363 K using the pulsed laser photolysis-laser-induced fluorescence (PLP-LIF) technique. The rate coefficient at room temperature was measured to be (1.14 ± 0.03) × 10-11 cm3 molecule-1 s-1, and the Arrhenius expression was derived to be kexpt278-363K = (1.61 ± 0.35) × 10-13 exp{(1256 ± 236)/T} cm3 molecule-1 s-1. Computational calculations were performed to compute the kinetics of the titled reaction in the temperature range of 200-400 K using advanced methods incorporated with tunneling correction at the CCSD(T)/aug-cc-pVTZ//M06-2X/6-31+G(d,p) level of theory. The Arrhenius expression derived from the computationally calculated rate coefficients is ktheo200-400K = (1.59 ± 0.35) × 10-13exp{(1389 ± 62)/T} cm3 molecule-1 s-1. The feasibility of each reaction pathway was also determined using the calculated thermochemical parameters. Atmospheric implication parameters such as cumulative atmospheric lifetime and photochemical ozone creation potential were calculated and are discussed in this paper.

Investigation of kinetics of phenyl radicals with ethyl formate in the gas phase using cavity ring-down spectroscopy and theoretical methodologies.

The gas-phase kinetics of phenyl radical (·C6H5) with ethyl formate (HCO2Et, EF) was investigated experimentally using ultrasensitive laser-based cavity ring-down spectroscopy (CRDS). Phenyl radicals were generated by photolyzing nitrosobenzene (C6H5NO) at 248 nm and thereby probed at 504.8 nm. The rate coefficients for the (phenyl radical + EF) reaction were investigated between the temperatures of 260 and 361 K and at a pressure of 61 Torr with nitrogen (N2) as diluent. The temperature-dependent Arrhenius expression for the test reaction was obtained as: [Formula: see text]=(1.20  ±  0.16) × 10-13 exp[-(435.6  ±  50.0)/T] cm3 molecule-1 s-1 and the rate coefficient at room temperature was measured out to be: [Formula: see text]=(4.54  ±  0.42) × 10-14 cm3 molecule-1 s-1. The effects of pressure and laser fluence on the kinetics of the test reaction were found to be negligible within the experimental uncertainties. To complement the experimental findings, kinetics for the reaction of phenyl radicals with EF was investigated theoretically using Canonical Variational Transition State Theory (CVT) with Small Curvature Tunnelling (SCT) at CCSD(T)/cc-pVDZ//B3LYP/6-31 + G(d,p) level of theory in the temperatures between 200 and 400 K. The theoretically calculated rate coefficients for the title reaction were expressed in the Arrhenius form as: [Formula: see text]= (1.48  ±  0.56) × 10-38 × T8.47 × exp[(2431.3  ±  322.0)/T] cm3 molecule-1 s-1 and the corresponding rate coefficient at room temperature was calculated to be: [Formula: see text]= 4.91 × 10-14 cm3 molecule-1 s-1. A very good agreement was observed between the experimentally measured and theoretically calculated rate coefficients at 298 K. Thermochemical parameters as well as branching ratios for the reaction of (phenyl radical + EF) are also discussed in this manuscript.

Kinetic Investigations of the Reaction of Phenyl Radicals with Ethyl Acetate in the Gas Phase: An Experimental and Computational Study.

Cavity ring-down spectroscopy (CRDS) was employed to investigate the kinetics of the reaction between phenyl radicals (C6H5•) and ethyl acetate (EtOAc) in the gas phase. Nitrosobenzene (C6H5NO) was used as the radical precursor to generate C6H5• at 248 nm, and the generated radicals were subsequently probed at 504.8 nm. The rate coefficients were investigated experimentally in the temperature range of 258-358 K with an interval of 20 K and at a total pressure of 55 Torr in the nitrogen atmosphere. The obtained Arrhenius expression for the title reaction (C6H5• + EtOAc) in the temperature range of 258-358 K was kphenyl + EtOAcExpt - (258 - 358 K) = (9.33 ± 0.11) × 10-16 exp[(883.7 ± 181.0)/T] cm3 molecule-1 s-1, and the rate coefficient at room temperature (298 K) was kphenyl + EtOAcExpt - 298 K = (2.20 ± 0.12) × 10-14 cm3 molecule-1 s-1. Negligible effects of pressure and photolysis laser fluence were found on the experimentally measured rate coefficients. To complement our experimental findings, rate coefficients of the title reaction were computationally investigated employing the canonical variational transition-state theory with small curvature tunnelling (CVT/SCT) at the CCSD(T)/cc-pVDZ//B3LYP/6-31+G(d,p) level of theory in the temperature range of 200-400 K. The temperature-dependent rate coefficient in the studied temperature range was obtained to be kphenyl + EtOAcTheory - (200 - 400 K) = (7.68 ± 0.12) × 10-17 exp[(1731.6 ± 216.0)/T] cm3 molecule-1 s-1, and the rate coefficient at 298 K was obtained as kphenyl + EtOAcTheory - 298 K = 2.45 × 10-14 cm3 molecule-1 s-1. Both the experimentally measured and computed rate coefficients show good agreement at 298 K. A negative temperature dependency was observed for both the experimentally measured and computed rate coefficients. A detailed discussion of the thermochemical parameters and branching ratios of the title reaction are also presented in this Article.

Investigation of the Absorption Cross Section of Phenyl Radical and Its Kinetics with Methanol in the Gas Phase Using Cavity Ring-Down Spectroscopy and Theoretical Methodologies.

Cavity ring-down spectroscopy (CRDS) was used to measure the absorption cross section of phenyl radicals (C6H5•) at 504.8 nm (2B1 ← 2A1 transition) in the nitrogen atmosphere at 40 Torr total pressure and 298 K using nitrosobenzene (C6H5NO) as the radical precursor. At 504.8 nm, the absorption cross section was measured to be σphenyl504.8 nm = (5.7 ± 1.4) × 10-19 cm2 molecule-1. The absorption cross section was independent of the total pressure range (40-200 Torr) over which it was studied with a precursor concentration of (4-5) × 1013 molecules cm-3. In addition to this, the absolute rate coefficients for the reaction of phenyl radicals with methanol were measured over the temperature range of 263-298 K and at 40 Torr pressure with N2 using CRDS. The temperature-dependent rate coefficient for the title reaction over the studied temperature range was obtained to be k263-298 Kexperiment (T) = (1.38 ± 0.60) × 10-11 exp [-(1764 ± 321)/T] cm3 molecule-1 s-1 with a rate coefficient of k(T) = (3.50 ± 0.32) × 10-14 cm3 molecule-1 s-1 at 298 K. The effect of pressure and laser fluence was found to be negligible within the experimental uncertainties in the studied range. In addition, to complement our experimental findings, the T-dependent rate coefficients for the title reaction were investigated using computational methods. The B3LYP/6-311 + G(d,p) level of theory was used in combination with canonical variational transition-state theory with small-curvature tunneling to calculate the rate coefficients. The T-dependent rate coefficient in the range of 200-400 K was obtained as k200-400 Ktheory (T) = 2.43 × 10-13 exp[-(478.38/T)] cm3 molecule-1 s-1 with a room-temperature (298 K) rate coefficient of 4.67 × 10-14 cm3 molecule-1 s-1.

DCAF1 (VprBP): emerging physiological roles for a unique dual-service E3 ubiquitin ligase substrate receptor.

Cullin-RING ligases (CRLs) comprise a large group of modular eukaryotic E3 ubiquitin ligases. Within this family, the CRL4 ligase (consisting of the Cullin4 [CUL4] scaffold protein, the Rbx1 RING finger domain protein, the DNA damage-binding protein 1 [DDB1], and one of many DDB1-associated substrate receptor proteins) has been intensively studied in recent years due to its involvement in regulating various cellular processes, its role in cancer development and progression, and its subversion by viral accessory proteins. Initially discovered as a target for hijacking by the human immunodeficiency virus accessory protein r, the normal targets and function of the CRL4 substrate receptor protein DDB1-Cul4-associated factor 1 (DCAF1; also known as VprBP) had remained elusive, but newer studies have begun to shed light on these questions. Here, we review recent progress in understanding the diverse physiological roles of this DCAF1 in supporting various general and cell type-specific cellular processes in its context with the CRL4 E3 ligase, as well as another HECT-type E3 ligase with which DCAF1 also associates, called EDD/UBR5. We also discuss emerging questions and areas of future study to uncover the dynamic roles of DCAF1 in normal physiology.

VprBP (DCAF1): a promiscuous substrate recognition subunit that incorporates into both RING-family CRL4 and HECT-family EDD/UBR5 E3 ubiquitin ligases.

The terminal step in the ubiquitin modification system relies on an E3 ubiquitin ligase to facilitate transfer of ubiquitin to a protein substrate. The substrate recognition and ubiquitin transfer activities of the E3 ligase may be mediated by a single polypeptide or may rely on separate subunits. The latter organization is particularly prevalent among members of largest class of E3 ligases, the RING family, although examples of this type of arrangement have also been reported among members of the smaller HECT family of E3 ligases. This review describes recent discoveries that reveal the surprising and distinctive ability of VprBP (DCAF1) to serve as a substrate recognition subunit for a member of both major classes of E3 ligase, the RING-type CRL4 ligase and the HECT-type EDD/UBR5 ligase. The cellular processes normally regulated by VprBP-associated E3 ligases, and their targeting and subversion by viral accessory proteins are also discussed. Taken together, these studies provide important insights and raise interesting new questions regarding the mechanisms that regulate or subvert VprBP function in the context of both the CRL4 and EDD/UBR5 E3 ligases.